Gene Expression
Nebulas
Gene Expression NebulasSummary: RNAseq profiling of seeds and 7 time points during germination in rice under aerobic and anerobic conditions, as well as following re-oxygenation.
Overall Design: Total RNA was extracted from samples collected at each time point in triplicate. The time points were: 0 h (dry seed), 1 h, 3 h, 12 h, 24 h, 2 days, 3 days and 4 days under aerobic (A) and anaerobic (N) conditions, as well as 3‐day‐old seedlings grown under anaerobic conditions that were switched to air for 1 day.
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| Growth Protocol: | Rice (Oryza sativa ‘Amaroo’) was de‐hulled, surface sterilised and grown in culture medium [0.5 mm 2‐(N‐morpholine)‐ethanesulphonic acid (MES), 0.4 mm CaSO4, pH 6.5) that was bubbled with air or nitrogen gas (N2) (6–7 L min−1). |
| Treatment Protocol: | For the dry seed and time points up to 24 h, the embryos were rapidly dissected and snap frozen. For all time points after that (2, 3 and 4 days and 3dN1dA) only whole coleoptiles were sampled and snap frozen. For these later time points (under aerobic conditions) primary leaf tissue was removed and only coleoptiles were harvested. |
| Extract Protocol: | RNA isolation was carried out using the Sigma Spectrum Plant Total RNA kit. |
| Library Construction Protocol: | TruSeq Stranded Total RNA with Ribo‐Zero Plant Sample Prep Kits were used to generate the libraries, according to manufacturer’s instructions (Illumina). rRNAs removed, random fragmentation, stranded library |
| Molecule Type: | rRNA- RNA |
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| Library Layout: | SINGLE |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 1500 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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